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54 results for “cytochrome oxidase subunit I”
FIGURE 1. Neighbor-joining tree for cytochrome c oxidase subunit I in Anacroneuria flintorum Froehlich 2002 (Plecoptera: Perlidae): Notes, distribution, and life stages association using molecular tools
FIGURE 1. Neighbor-joining tree for cytochrome c oxidase subunit I (COI) sequences (433 bp) from Anacroneuria flintorum Froehlich and related stoneflies from Espírito Santo and São Paulo States, Brazil, modeled by Kimura-2-parameter (K2P).
FIGURE 7. Cytochrome oxidase subunit I in A new species of small-eared shrew of the genus Cryptotis (Mammalia, Eulipotyphla, Soricidae) from the northernmost Peruvian Andes
FIGURE 7. Cytochrome oxidase subunit I phylogenetic trees for Cryptotis genus. Bootstrap supports are indicated at each node for A. Maximum Likelihood; B. Posterior Probability values for Bayesian Inference.
Table 2. Genetic distances for mitochondrial DNA partial cytochrome c oxidase subunit I and cytochrome b in Molecular phylogeny of the Aplodactylidae (Perciformes: Cirrhitoidea), a group of Southern Hemisphere marine ® shes
<p>Table 2. Genetic distances for mitochondrial DNA partial cytochrome <i>c</i> oxidase subunit I and cytochrome <i>b</i> sequences when combined. Values are Kimura (1980) two-parameter percentage sequence divergences, obtained when using the optimum expected transition±transversion nucleotide substitution ratio of 3.0 from maximum likelihood analysis (fi gure 3).</p><table><tbody><tr><th></th><th></th><th>1</th><th>2</th><th>3</th><th>4</th><th>5</th><th>6</th><th>7</th></tr></tbody><tbody><tr><th>1</th><td><i>Aplodactylus arctidens</i></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>2</th><td><i>Aplodactylus punctatus</i></td><td>6.1</td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>3</th><td><i>Aplodactylus westralis</i></td><td>7.8</td><td>7.6</td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>4</th><td><i>Aplodactylus etheridgii</i></td><td>10.0</td><td>10.3</td><td>10.0</td><td></td><td></td><td></td><td></td></tr><tr><th>5</th><td><i>Aplodactylus lophodon</i></td><td>11.8</td><td>11.9</td><td>12.4</td><td>11.1</td><td></td><td></td><td></td></tr><tr><th>6</th><td><i>Chironemus marmoratus</i></td><td>20.0</td><td>18.7</td><td>18.3</td><td>19.3</td><td>19.5</td><td></td><td></td></tr><tr><th>7</th><td><i>Cheilodactylus fasciatus</i></td><td>21.8</td><td>21.0</td><td>20.5</td><td>22.6</td><td>20.2</td><td>21.2</td><td></td></tr><tr><th>8</th><td><i>Cirrhitus splendens</i></td><td>22.6</td><td>20.7</td><td>21.0</td><td>23.1</td><td>22.0</td><td>23.1</td><td>22.8</td></tr></tbody></table>
Data from: Site specific distribution of oak rhizosphere associated oomycetes revealed by cytochrome c oxidase subunit II metabarcoding
The phylum Oomycota comprises important tree pathogens like Phytophthora quercina, involved in central European oak decline, and P. cinnamomi shown to affect holm oaks among many other hosts. Despite the importance to study the distribution, dispersal and niche partitioning of this phylum, metabarcoding surveys and studies considering environmental factors that could explain oomycete community patterns are still rare. We investigated oomycetes in the rhizosphere of evergreen oaks in a Spanish oak woodland using metabarcoding based on Illumina sequencing of the taxonomic marker cytochrome c oxidase subunit II (cox2). We developed an approach amplifying a 333 bp long fragment using the forward primer Hud-F (Hudspeth, Nadler, & Hudspeth, 2000) and a reverse primer found using DegePrime (Hugerth et al., 2014). Factors reflecting topo-edaphic conditions and tree health were linked to oomycete community patterns. The majority of detected OTUs belonged to the Peronosporales. Most taxa were relatives of the Pythiaceae, but relatives of the Peronosporaceae and members of the Saprolegniales were also found. The most abundant OTUs were related to Globisporangium irregulare and Phytophthora cinnamomi, both displaying strong site specific patterns. Oomycete communities were strongly correlated with the environmental factors: altitude, crown foliation, slope and soil skeleton and soil nitrogen. Our findings illustrate the significance of small scale variation in habitat conditions for the distribution of oomycetes and highlights the importance to study oomycete communities in relation to such ecological patterns.
Figure 6. The maximum-likelihood phylogram for cytochrome oxidase subunit I in A case of biodiversity overestimation in the Balkan Belgrandiella A. J. Wagner, 1927 (Caenogastropoda: Hydrobiidae): molecular divergence not paralleled by high morphological variation
Figure 6. The maximum-likelihood phylogram for cytochrome oxidase subunit I (COI) haplotypes. Bootstrap support and Bayesian posterior probabilities are shown. Normal font indicates reference haplotypes, bold font indicates haplotypes obtained in present study.
Figure 5. Minimum spanning haplotype network derived from a 658 base-pair cytochrome c oxidase subunit I in Six degrees of separation in barnacles? Assessing genetic variability in the sea-turtle epibiont Stomatolepas elegans (Costa) among turtles, beaches and oceans
Figure 5. Minimum spanning haplotype network derived from a 658 base-pair cytochrome c oxidase subunit I (COI) fragment from 57 Stomatolepas elegans collected from nine different Lepidochelys olivacea nesting on Playa Teopa, Jalisco, Mexico, six S. elegans from Caretta caretta from the western Atlantic, and six S. praegustator from C. caretta from the western Atlantic. Circle sizes are proportional to the frequency of each haplotype, with haplotype 1 being most common. Coloured pie slices are also proportional, and represent the number of S. elegans from each turtle characterized by the respective haplotype. Colours represent the nine Mexican turtles randomly sampled for S. elegans populations. Open circles with numbers indicate Atlantic haplotypes. Solid black circles designate hypothetical missing haplotypes. The network includes S. elegans haplotypes 1–21, and S. praegustator haplotypes 19, 26–30. Haplotypes 1–17, shown in colour, represent Jalisco, Mexico specimens collected from nine different turtles in the Pacific, and haplotypes 18–21 and 26–30, shown as unshaded circles, represent southeastern United States Atlantic specimens collected from six different C. caretta (see Table 1).
Figure 7. Maximum likelihood phylogram for combined 18S and cytochrome oxidase subunit I in An unusual, flagellum-bearing hydrobiid snail (Gastropoda: Rissooidea: Hydrobiidae) from Greece, with descriptions of a new genus and a new species
Figure 7. Maximum likelihood phylogram for combined 18S and cytochrome oxidase subunit I (COI) sequences, bootstrap support.
Figure 6. Maximum likelihood phylogram for cytochrome oxidase subunit I in An unusual, flagellum-bearing hydrobiid snail (Gastropoda: Rissooidea: Hydrobiidae) from Greece, with descriptions of a new genus and a new species
Figure 6. Maximum likelihood phylogram for cytochrome oxidase subunit I (COI) sequences, bootstrap support (1000 replicates).
Figure 5. Maximum likelihood trees constructed from mitochondrial cytochrome c oxidase subunit I in Cryptic diversity in coastal Australasia: a morphological and mitonuclear genetic analysis of habitat-forming sibling species
Figure 5. Maximum likelihood trees constructed from mitochondrial cytochrome c oxidase subunit I (left; log likelihood: -399.5730) and nuclear adenine nucleotide transporter intron (right; log likelihood: -12170.8682) sequences of Pyura praeputialis and Pyura doppelgangera sp. nov. Nodal support from 1000 bootstrap replications (> 75%) is indicated next to some branches. Circles indicate regions in which a particular allele was present. For simplicity, allele frequencies are not indicated.
FIGURE 2. The Neighbor-Joining tree for the cytochrome oxidase c subunit 1 in Mitochondrial diversity of the white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in Vietnam
FIGURE 2. The Neighbor-Joining tree for the cytochrome oxidase c subunit 1 (COI) gene fragment. The bootstrap values (≥ 50 %) obtained from 1000 pseudoreplications are presented above the branches. Crocidura olivieri is used as outgroup.
Figure 2. Minimum-evolution tree deduced from cytochrome c oxidase subunit I in DNA barcoding and morphology reveal exceptional species diversity of Scoparia (Lepidoptera: Crambidae) from the Hailuogou Glacier area, China
Figure 2. Minimum-evolution tree deduced from cytochrome c oxidase subunit I (COI) gene sequences. Sequences were corrected with the Kimura two-parameter substitution model. Codon positions included were 1st + 2nd + 3rd + noncoding. Values represented at the nodes of branches are bootstrap values (1000 replicates).
Figure 1. Neighbour-joining tree deduced from the cytochrome c oxidase subunit I in DNA barcoding and morphology reveal exceptional species diversity of Scoparia (Lepidoptera: Crambidae) from the Hailuogou Glacier area, China
Figure 1. Neighbour-joining tree deduced from the cytochrome c oxidase subunit I (COI) gene sequences using MEGA 5. Sequences were corrected with the Kimura two-parameter substitution model. Codon positions included were 1st + 2nd + 3rd + noncoding. Values represented at the nodes of branches are bootstrap values (1000 replicates).
Figure 3. Cytochrome c oxidase subunits I and II in Songs, genetics, and morphology: revealing the taxonomic units in the European Cicadetta cerdaniensis cicada group, with a description of new taxa (Hemiptera: Cicadidae)
Figure 3. Cytochrome c oxidase subunits I and II (COI and COII) mitochondrial DNA concatenated phylogeny of the Cicadetta cerdaniensis song group. Maximum-likelihood (ML, GARLI) phylogenies are shown with ML branch lengths (box on the left) and ML bootstrap support. Nodes with less than 50% bootstrap support have been collapsed. Cicadetta fangoana was selected as the out-group taxon; taxa colours correspond to Figure 9. Specimen names include two-letter country codes followed by species or informal names (later in this study: 'cerdaniensis'-like = Cicadetta sibillae sp. nov., 'intermediate' = Cicadetta anapaistica lucana ssp. nov.). Specimen identification numbers are congruent with the type series for undescribed taxa. Cicadetta cantilatrix specimens originate from Switzerland, France, Poland, Slovenia, Macedonia, and Bulgaria. Type localities of Cicadetta cantilatrix, Cicadetta cerdaniensis, and Cicadetta anapaistica are included.
Figure 10. Haplotype parsimonious networks constructed from cytochrome c oxidase subunit I in A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae)
Figure 10. Haplotype parsimonious networks constructed from cytochrome c oxidase subunit I sequences of 30 specimens of: A, Gigantopelta chessoia sp. nov.; B, Gigantopelta aegis sp. nov. Open circles are represented haplotypes, number inside the circles and sizes of the circles correspond to number of individuals sharing the haplotype. Filled circles are hypothesized intermediate haplotypes that are not represented by sequences.
Figure 5. Phylogenetic relationships inferred from cytochrome c oxidase subunit I in Pseudocryptic speciation of Chrysochroa fulgidissima (Coleoptera: Buprestidae) with two new species from Korea, China and Vietnam
Figure 5. Phylogenetic relationships inferred from cytochrome c oxidase subunit I + 16S ribosomal RNA gene (1193 bp). Labelling as in Figure 3.
Figure 3. Phylogenetic relationships inferred from cytochrome c oxidase subunit I in Pseudocryptic speciation of Chrysochroa fulgidissima (Coleoptera: Buprestidae) with two new species from Korea, China and Vietnam
Figure 3. Phylogenetic relationships inferred from cytochrome c oxidase subunit I (664 bp). Colours represented within each terminal taxa denote biogeographical populations of Chrysochroa fulgidissima as given in Table 1. Numbers above branches are indicated by the neighbour-joining bootstrap value, Bayesian posterior probabilities, and the maximum likelihood bootstrap proportions. Numbers cited under branches are parsimony bootstrap symmetric resampling and jackknife support, respectively. The topology was constructed by Bayesian phylogenetic analysis.
Figure 2. Cytochrome oxidase c subunit I in An integrative approach to characterize cryptic species in the Thoracostoma trachygaster Hope, 1967 complex (Nematoda: Leptosomatidae)
Figure 2. Cytochrome oxidase c subunit I. Neighbourjoining tree based on P-distances with haplotypes from 2007 and the new haplotypes found in 2009 and 2010 (represented by numbers followed by clade – I, II, or III). The haplotypes from clade I and II that were recovered from 2007 appear underlined in the tree. The corresponding taxon names of the other clades can be found in Derycke et al. (2010a).
Figure 1. Best selected tree from a maximum likelihood reconstruction for the cytochrome c oxidase subunit I in Integrating DNA and morphological taxonomy to describe diversity in poorly studied microscopic animals: new species of the genus Abrochtha Bryce, 1910 (Rotifera: Bdelloidea: Philodinavidae)
Figure 1. Best selected tree from a maximum likelihood reconstruction for the cytochrome c oxidase subunit I data set under the general time reversible model with gamma distribution, displaying all compatible groupings and with average branch lengths proportional to numbers of substitutions per site, indicated by the scale bar. Bootstrap support values above 80% are shown below each branch; posterior probabilities above 0.8 from 36 000 sampled trees from the Bayesian analysis are shown above each branch. Support values for within-species relationships are not shown. Filled circles indicate clades (and singlets) identified by the 4¥ rule; open diamonds indicate clades (and singlets) identified by the generalized mixed yule coalescent model. Names refer to the species and the clonal populations.
FIGURE 3. Neighbor-joining tree for Cytochrome C Oxidase Subunit I in Two new species and three new provincial records of Neoperla (Plecoptera: Perlidae) from Nanling Mountains, China
FIGURE 3. Neighbor-joining tree for Cytochrome C Oxidase Subunit I (COI) sequences (659 bp) from Neoperla annulatispina Mo, Li & Wang, sp. nov. and N. nigromarginata Li & Zhang, 2014, modeled by Kimura-2-parameter (K2P).
FIGURE 8—Phylogenetic tree inferred using Bayesian Inference derived from cytochrome c oxidase subunit I in How many species of genus Lernaeopoda Blainville, 1822 (Siphonostomatoida: Lernaeopodidae) are there in the southwestern Atlantic?
FIGURE 8—Phylogenetic tree inferred using Bayesian Inference derived from cytochrome c oxidase subunit I (COI) gene dataset. Numbers in the nodes represent posterior probability (<0.95 are not shown).
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